density

`DensityFilterQuery` `dataclass`

Query for filtering AlphaFoldDB structures based on density confidence.

Parameters:

Name	Type	Description	Default
`confidence`	`float`	The confidence threshold for filtering residues. Residues with a pLDDT (b-factor) above this value are considered high confidence.	required
`min_threshold`	`int`	The minimum number of high-confidence residues required to keep the structure.	required
`max_threshold`	`int`	The maximum number of high-confidence residues allowed to keep the structure.	required

Result of filtering AlphaFoldDB structures based on density confidence.

Parameters:

Name	Type	Description	Default
`pdb_file`	`str`	The name of the PDB file that was processed.	required
`count`	`int`	The number of residues with a pLDDT above the confidence threshold.	required
`density_filtered_file`	`Path \| None`	The path to the density filtered PDB file, if passed filter.	`None`

Filter AlphaFoldDB structures based on density confidence.

Parameters:

Name	Type	Description	Default
`alphafold_pdb_files`	`list[Path]`	List of PDB files from AlphaFoldDB to filter.	required
`query`	`DensityFilterQuery`	The density filter query containing the confidence thresholds.	required
`density_filtered_dir`	`Path`	Directory where the filtered PDB files will be saved.	required

Yields:

Type	Description
`Generator[DensityFilterResult]`	For each PDB files yields whether it was filtered or not, and number of residues with pLDDT above the confidence threshold.